The question of how best to help babies who have been exposed to drugs in the womb — including prescription pain medications, antidepressants and illicit drugs like methamphetamine and cocaine — can be an emotionally charged issue. Bringing science to bear on the issue, the American Academy of Pediatrics has just updated its guidelines on treating these infants.

The number of babies experiencing drug-related symptoms after birth has risen by 45% since 1995, according to data compiled by the Agency for Healthcare Research and Quality. The rise may be attributed in part to increased maternal drug misuse and addiction, as well as to greater legitimate use of medication to treat pain and depression. Further, more careful surveillance for symptoms associated with maternal drug use have turned up more affected babies.

About 1% of pregnant women report recreational use of opioid painkillers like Oxycontin, according to the National Household Survey on Drug Use and Health, a number that has stayed constant since 2003. The new treatment guidelines, appearing on Monday in the journal Pediatrics, recommend that pregnant women addicted to prescription pain relievers or heroin should be maintained on either methadone or buprenorphine (Suboxone, Subutex). These recommendations are in line with prior consensus documents from the National Institutes on Health and World Health Organization.

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The authors state that the alternative to maintenance — active or passive detoxification — is “associated with increased risk of fetal distress and fetal loss.” However, 55% to 94% of babies prenatally exposed to opioids (that includes the maintenance drugs methadone and buprenorphine) will experience at least some withdrawal symptoms after birth. For mild withdrawal, the authors recommend simply providing a calm, nurturing environment to maximize infant sleep. In severe cases, the guidelines recommend that doctors provide tapered doses of methadone or morphine to the infant to minimize distress.

Breastfeeding may also help these babies: mothers maintained on methadone or buprenorphine will pass on small doses of the drug to their child, which can help reduce withdrawal. The child can be weaned from the drug entirely as he or she is weaned from the breast, or as the mother lowers her dose. The guidelines suggest encouraging breastfeeding unless there are other reasons to avoid it.

Although there is not much research on the question, the studies that do exist do not link the severity of withdrawal symptoms in these infants with later developmental problems.

The new guidelines also address the use of antidepressants in pregnancy, which can cause problems for some infants, especially when they are taken in the third trimester. This class of drugs, which includes Prozac, Zoloft and Paxil — the selective serotonin reuptake inhibitors — increases levels of the neurotransmitter serotonin in the brain.

The authors report that some exposed infants experience frequent crying, irritability, sleep disturbances and seizures, but the problem usually resolves itself within two weeks. The authors also note that the evidence does not suggest long-term harm from maternal use of antidepressants during pregnancy. They write:

Several recent reviews have not identified adverse neurodevelopmental outcomes among infants born to women treated with SSRI’s during pregnancy. SSRI treatment should be continued at the lowest effective dose because withdrawal of medication may have harmful effects on the mother infant [bond].The problems experienced by babies exposed to antidepressants in utero may not be caused by drug withdrawal at all, since the babies’ symptoms are more consistent with exposure to too much serotonin, not too little, as would be expected if withdrawal from antidepressants were the culprit.

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As for cocaine and other stimulants like methamphetamine, the authors report that exposure to such drugs does not produce a “clearly defined” withdrawal syndrome in babies. (In some studies, observers failed to detect specific problems in babies, unless they were specifically told the babies had been exposed to cocaine.) While some studies have found subtle differences in behavior in cocaine-exposed children, these are comparable in scale to those seen in babies born to women who smoked cigarettes while pregnant.

The new guidelines note that state laws vary on whether mothers or babies can be tested for drugs without consent. Although physicians are advised to “avoid discriminatory practices,” the new recommendations fail to address how drug-testing mothers to determine whether a baby is experiencing withdrawal may lead to unintended negative consequences for both parties.

In some states, infants can be taken from their mothers after a positive drug test, even in the absence of evidence of child abuse. This, despite data showing that mother-infant bonding has a far greater effect on child outcomes than drug exposure. Overwhelmingly, the women who are tested for drug use involuntarily and who lose custody due to the results are poor or minorities.

Moreover, there’s no evidence that putting these children in foster care improves outcomes. Indeed, studies of children in “borderline” cases, in which investigators were unsure whether or not to remove them, find that those who end up staying with their parents have far better long-term outcomes than those who are removed.

This month, 50 medical and public policy organizations and child welfare experts filed an Amicus Curiae brief in the state of New Jersey, siding with a mother who was accused of child abuse solely on the grounds of a positive cocaine test when she gave birth. They note that such testing policies typically backfire because they deter drug-using women from seeking prenatal care, which is the most effective way of reducing drug-related harm to their infants

As the American College of Obstetrics and Gynecology (a party to the Amicus brief) put it in a policy statement on its website: “Seeking obstetric–gynecologic care should not expose a woman to criminal or civil penalties, such as incarceration, involuntary commitment, loss of custody of her children, or loss of housing.”

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Indeed, research on children exposed to crack during pregnancy has found that the kids who do best later in life are not those whose mothers took the least cocaine during pregnancy. Instead, it is those whose mothers refrain from drug use during their babies’ early childhood. Both mothers and children do better when they receive supportive, nonjudgmental access to addiction treatment and other health care — not when they are unduly stigmatized because of drug use.

Indeed, the stigma associated with labeling infants as “drug addicted” (a term that is inaccurate, since babies are not capable of continuing to use drugs despite negative consequences — a condition that is required to meet the medical definition of addiction) can often produce greater harm than the drugs themselves. Giving a child the label “crack baby,” for example, has been shown to lead even trained adults to view that child’s normal behavior as pathological.

Moreover, the drug that consistently causes the most permanent and irreversible damage in utero is alcohol — and yet no one takes babies away from their parents for a positive breathalyzer test at birth. Nonetheless, fetal alcohol spectrum disorder remains the leading known preventable cause of intellectual disability, affecting 1% of all babies, about one-third of them severely.

Maia Szalavitz is a health writer for TIME.com. Find her on Twitter at @maiasz. You can also continue the discussion on TIME Healthland‘s Facebook page and on Twitter at @TIMEHealthland.